Alan McCormack had just cancelled out Anthony Sweeney's first-half opener for Pools when Collins appeared to elbow Lee Barnard in the face in an off the ball incident.
Referee Gavin Mayo consulted his assistant before sending Collins off and from the resulting free-kick Southend scored the winning goal.
Charlie Mulgrew side footed the free-kick to Nicky Bailey on the left of the penalty area and his right-foot shot beat Jan Budtz at his near post.
Hartlepool opened the scoring in the ninth minute when Alan Thompson's cross from the left evaded everyone except Sweeney, who scored from the far post despite Peter Clarke's attempt to clear off the line.
And Pools may have gone in 2-0 up when a Thompson free-kick from the right was headed just wide by Richie Barker.
Southend had their chances to score with Bailey being denied by a Budtz save and Richie Humhpreys blocking a Barnard effort.
The Shrimpers equalised in the 61st minute when Mark Gower nudged the ball forward to Alex Revell on the left.
He spotted McCormack on the edge of the box and the midfielder unleashed a shot that gave Budtz no chance.
Ten-man Pools bravely battled to find an equaliser of their own. Manager Danny Wilson made three substitutions to bring on some fresh legs and Barker went agonisingly close to getting a leveller but his header was inches wide.
But ultimately, the visitors were unable to stop the Blues avenging the 4-3 defeat they suffered at Victoria Park three weeks ago.